RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 023905
(275 letters)
>gnl|CDD|234564 PRK00001, rplC, 50S ribosomal protein L3; Validated.
Length = 210
Score = 285 bits (733), Expect = 4e-98
Identities = 103/212 (48%), Positives = 144/212 (67%), Gaps = 5/212 (2%)
Query: 60 IGVMGTKLGMMSYFEPDGTVVPVTVVGFREGNIVTQVKTEATDGYDAVQIGYRRVRDKKL 119
G++G K+GM F DG +PVTV+ N+VTQVKT DGY+AVQ+G+ ++K++
Sbjct: 3 KGILGKKVGMTQIFTEDGESIPVTVIEA-GPNVVTQVKTVEKDGYNAVQLGFGDKKEKRV 61
Query: 120 TKPELGHLQKSGLIPMRHLQEFRLQSIDGFEAGQKLAFEEIFNEGDLVDVSGTTIGKGFQ 179
KPE GH K+G+ P RHL+EFR+ ++ +E GQ++ +IF G VDV+GT+ GKGF
Sbjct: 62 NKPEAGHFAKAGVEPKRHLREFRV--VEEYEVGQEIT-VDIFEAGQKVDVTGTSKGKGFA 118
Query: 180 GGIKRHNFRRGAMTHG-SKSHRQLGSIGAGTTPGRVYKGKKMPGRMGGTTRKIRKLKIVK 238
G IKRHNF G +HG S+SHR+ GSIGA TPGRV+KGKKM G MG ++ L++VK
Sbjct: 119 GVIKRHNFSGGPASHGNSRSHRRPGSIGARQTPGRVFKGKKMAGHMGNERVTVQNLEVVK 178
Query: 239 IDNDLRVVMIKGAVPGKPGNLLRVAPAKIVGK 270
+D + ++++KGAVPG G L+ + PA K
Sbjct: 179 VDAERNLLLVKGAVPGAKGGLVIIKPAVKAKK 210
>gnl|CDD|234285 TIGR03625, L3_bact, 50S ribosomal protein L3, bacterial. This
model describes bacterial (and mitochondrial and
chloroplast) class of ribosomal protein L3. A separate
model describes the archaeal form, where both belong to
Pfam family pfam00297. The name is phrased to meet the
needs of bacterial genome annotation. Organellar forms
typically will have transit peptides, N-terminal to the
region modeled here.
Length = 202
Score = 277 bits (711), Expect = 7e-95
Identities = 100/203 (49%), Positives = 139/203 (68%), Gaps = 3/203 (1%)
Query: 61 GVMGTKLGMMSYFEPDGTVVPVTVVGFREGNIVTQVKTEATDGYDAVQIGYRRVRDKKLT 120
G++G K+GM F DG VPVTV+ N+VTQVKT DGY AVQ+G+ ++K++
Sbjct: 1 GLLGKKVGMTQIFTEDGKAVPVTVIEV-GPNVVTQVKTVEKDGYSAVQLGFGEKKEKRVN 59
Query: 121 KPELGHLQKSGLIPMRHLQEFRLQSIDGFEAGQKLAFEEIFNEGDLVDVSGTTIGKGFQG 180
KPE GH K+G+ P RHL+EFR+ ++G+E G ++ +IF G VDV+GT+ GKGF G
Sbjct: 60 KPEAGHFAKAGVEPKRHLREFRVDDLEGYEVGDEIT-VDIFEAGQKVDVTGTSKGKGFAG 118
Query: 181 GIKRHNFRRGAMTHG-SKSHRQLGSIGAGTTPGRVYKGKKMPGRMGGTTRKIRKLKIVKI 239
+KRHNF G +HG SKSHR GSIG TPGRV+KGKKM G MG ++ L++VK+
Sbjct: 119 VMKRHNFSGGPASHGNSKSHRAPGSIGQRQTPGRVFKGKKMAGHMGNERVTVQNLEVVKV 178
Query: 240 DNDLRVVMIKGAVPGKPGNLLRV 262
D + ++++KGAVPG G+L+ +
Sbjct: 179 DAERNLLLVKGAVPGAKGSLVLI 201
>gnl|CDD|177065 CHL00143, rpl3, ribosomal protein L3; Validated.
Length = 207
Score = 268 bits (686), Expect = 5e-91
Identities = 118/208 (56%), Positives = 161/208 (77%), Gaps = 4/208 (1%)
Query: 60 IGVMGTKLGMMSYFEPDGTVVPVTVVGFREG-NIVTQVKTEATDGYDAVQIGYRRVRDKK 118
IG++GTK+GM F+ G +PVT++ + G ++TQ+KT TDGY+A+QIGY++V KK
Sbjct: 3 IGLLGTKIGMTQIFDETGNAIPVTIL--KVGPCVITQIKTLTTDGYNAIQIGYKQVSTKK 60
Query: 119 LTKPELGHLQKSGLIPMRHLQEFRLQSIDGFEAGQKLAFEEIFNEGDLVDVSGTTIGKGF 178
LTKP+LGHLQKS + P+++L+EFR++S + FE GQ L + F+ G LV+VSG +IGKGF
Sbjct: 61 LTKPQLGHLQKSNVPPLKYLKEFRVKSSEEFEVGQPLT-VDAFSVGQLVNVSGKSIGKGF 119
Query: 179 QGGIKRHNFRRGAMTHGSKSHRQLGSIGAGTTPGRVYKGKKMPGRMGGTTRKIRKLKIVK 238
G KRHNF RG MTHGSK+HR GSIGAGTTPGRVY GKKM GR+G I+ LKI+K
Sbjct: 120 AGLQKRHNFSRGPMTHGSKNHRAPGSIGAGTTPGRVYPGKKMAGRLGNKKVTIKNLKILK 179
Query: 239 IDNDLRVVMIKGAVPGKPGNLLRVAPAK 266
+D++ ++++KG+VPGKPGNLL ++P+K
Sbjct: 180 VDSENNLLVLKGSVPGKPGNLLSISPSK 207
>gnl|CDD|223165 COG0087, RplC, Ribosomal protein L3 [Translation, ribosomal
structure and biogenesis].
Length = 218
Score = 241 bits (618), Expect = 1e-80
Identities = 102/219 (46%), Positives = 138/219 (63%), Gaps = 6/219 (2%)
Query: 60 IGVMGTKLGMMSYFEPDGTVVPVTVVGFREGNIVTQVKTEATDGYDAVQIGYRRVRDKKL 119
+G +G K+GM F+ G VPVTV+ N+V QVKT TDGY AVQ+G + K++
Sbjct: 2 LGFLGYKVGMTHVFDERGISVPVTVIEV-PPNVVVQVKTYETDGYRAVQVGAGDRKAKRV 60
Query: 120 TKPELGHLQKSGLIPMRHLQEFRLQSIDG---FEAGQKLAFEEIFNEGDLVDVSGTTIGK 176
KP +GH K+G+ P RHL EFR+ D FE GQ++ ++F EG+LVDV+G T GK
Sbjct: 61 NKPLVGHFAKAGVKPKRHLAEFRVGGGDVAEKFEVGQEI-TVDVFKEGELVDVTGVTKGK 119
Query: 177 GFQGGIKRHNFRRGAMTHGSK-SHRQLGSIGAGTTPGRVYKGKKMPGRMGGTTRKIRKLK 235
GFQG +KR F+ G +HGS SHR+ GSIG TPGRV+KGKKM G MG ++ L+
Sbjct: 120 GFQGVMKRWGFKGGPASHGSSLSHRRPGSIGQRQTPGRVFKGKKMAGHMGNERVTVQNLE 179
Query: 236 IVKIDNDLRVVMIKGAVPGKPGNLLRVAPAKIVGKNIPK 274
+VK+D + ++++KGAVPG L+ V PA K
Sbjct: 180 VVKVDVENNLILVKGAVPGAKKRLVVVRPAVKAKKKTSA 218
>gnl|CDD|144036 pfam00297, Ribosomal_L3, Ribosomal protein L3.
Length = 199
Score = 211 bits (539), Expect = 7e-69
Identities = 88/200 (44%), Positives = 120/200 (60%), Gaps = 5/200 (2%)
Query: 66 KLGMMSYF-EPDGTVVPVTVVGFREGNIVTQVKT--EATDGYDAVQIGYRRVRDKKLTKP 122
K GM F E G + PVTV+ +V QVKT E DGY A+Q+G ++ ++ K
Sbjct: 1 KAGMTHIFTEKKGVLEPVTVIEV-PPMVVVQVKTYEETNDGYKAIQVGLESIKKYRVVKR 59
Query: 123 ELGHLQKSGLIPMRHLQEFRLQSIDGFEAGQKLAFEEIFNEGDLVDVSGTTIGKGFQGGI 182
LGH QK G P H+ EFR+ + FE GQ +A ++F EG+ VDV+G T GKGFQG +
Sbjct: 60 VLGHTQKRGTPPKAHVMEFRVNGGEEFEPGQTIAVSDVFREGEYVDVTGVTKGKGFQGVM 119
Query: 183 KRHNFRRGAMTHGSKSHRQLGSIGAGTTPGRVYKGKKMPGRMGGTTRKIRKLKIVKIDND 242
KR F+R HG HR+ GSIGA PGRV+ G KM G+MG R + LKI +ID +
Sbjct: 120 KRWGFKRLPRKHGRGYHRKPGSIGAW-HPGRVFPGVKMAGQMGNHHRTEQNLKIYRIDQE 178
Query: 243 LRVVMIKGAVPGKPGNLLRV 262
++++KG+VPG L+ +
Sbjct: 179 NNLLLVKGSVPGPKKRLVTI 198
>gnl|CDD|234286 TIGR03626, L3_arch, archaeal ribosomal protein L3. This model
describes exclusively the archaeal class of ribosomal
protein L3. A separate model (TIGR03625) describes the
bacterial/organelle form, and both belong to Pfam family
pfam00297. Eukaryotic proteins are excluded from this
model [Protein synthesis, Ribosomal proteins: synthesis
and modification].
Length = 330
Score = 78.5 bits (194), Expect = 7e-17
Identities = 44/134 (32%), Positives = 61/134 (45%), Gaps = 23/134 (17%)
Query: 152 GQKLAFEEIFNEGDLVDVSGTTIGKGFQGGIKR---HNFRRGAMTHGSKSHRQLGSIGAG 208
G++++ ++F EG LVDV T GKGFQG +KR R K R +G++G
Sbjct: 179 GKEISVSDVFKEGQLVDVIAVTKGKGFQGVVKRWGVKLLPRKHKRR--KGGRHIGTLGP- 235
Query: 209 TTPGRVYKGKKMPGRMGGTTRKIRKLKIVKIDNDL-----------------RVVMIKGA 251
TP RV G+MG R +I+KI D V+IKG+
Sbjct: 236 WTPSRVRWTVPQAGQMGYHQRTEYNKRILKIGEDGDEITPKGGFVNYGLVRNDYVLIKGS 295
Query: 252 VPGKPGNLLRVAPA 265
VPG L+R+ A
Sbjct: 296 VPGPSKRLIRLRDA 309
>gnl|CDD|235260 PRK04231, rpl3p, 50S ribosomal protein L3P; Reviewed.
Length = 337
Score = 69.1 bits (170), Expect = 1e-13
Identities = 42/133 (31%), Positives = 61/133 (45%), Gaps = 21/133 (15%)
Query: 152 GQKLAFEEIFNEGDLVDVSGTTIGKGFQGGIKRHN--FRRGAMTHGSKSHRQLGSIGAGT 209
G++++ ++F EG LVDV T GKGFQG +KR R +G++G
Sbjct: 184 GKEISISDVFKEGQLVDVIAVTKGKGFQGVVKRWGVKLLPRKHKR-RGGSRHIGTLG-PW 241
Query: 210 TPGRVYKGKKMPGRMGGTTRKIRKLKIVKI-DNDLRV----------------VMIKGAV 252
P RV G+MG R +I+KI D+ + V+IKG+V
Sbjct: 242 NPSRVMWTVPQAGQMGFHQRTEYNKRILKIGDDGDEITPKGGFLHYGLVRNDYVLIKGSV 301
Query: 253 PGKPGNLLRVAPA 265
PG L+R+ PA
Sbjct: 302 PGPAKRLIRLRPA 314
>gnl|CDD|240267 PTZ00103, PTZ00103, 60S ribosomal protein L3; Provisional.
Length = 390
Score = 37.4 bits (87), Expect = 0.005
Identities = 27/83 (32%), Positives = 39/83 (46%), Gaps = 4/83 (4%)
Query: 160 IFNEGDLVDVSGTTIGKGFQGGIKRHNFRRGA-MTHGSKSHRQLGSIGAGTTPGRVYKGK 218
+F + +++DV G T G GF+G +KR R TH + R++ IGA P RV
Sbjct: 207 VFQQNEMIDVIGVTKGHGFEGVVKRWGVTRLPRKTH--RGLRKVACIGA-WHPARVQYTV 263
Query: 219 KMPGRMGGTTRKIRKLKIVKIDN 241
G+ G R KI +I
Sbjct: 264 PRAGQHGYHHRTELNKKIYRIGV 286
>gnl|CDD|130164 TIGR01092, P5CS, delta l-pyrroline-5-carboxylate synthetase. This
protein contains a glutamate 5-kinase (ProB, EC
2.7.2.11) region followed by a gamma-glutamyl phosphate
reductase (ProA, EC 1.2.1.41) region [Amino acid
biosynthesis, Glutamate family].
Length = 715
Score = 30.3 bits (68), Expect = 1.4
Identities = 15/52 (28%), Positives = 22/52 (42%), Gaps = 7/52 (13%)
Query: 88 REGNIVTQVKTEATDGYD-------AVQIGYRRVRDKKLTKPELGHLQKSGL 132
R G+I Q+ +DG + AV G +R+R + L LQK
Sbjct: 30 RLGSICEQLSELNSDGREVILVTSGAVAFGRQRLRHRILVNSSFADLQKPQP 81
>gnl|CDD|217140 pfam02608, Bmp, Basic membrane protein. This is a family of basic
membrane lipoproteins form Borrelia and various putative
lipoproteins form other bacteria. All of these proteins
are outer membrane proteins and are thus antigenic in
nature when possessed by the pathogenic members of the
family.
Length = 305
Score = 28.9 bits (65), Expect = 2.7
Identities = 14/62 (22%), Positives = 20/62 (32%), Gaps = 10/62 (16%)
Query: 54 MSYEAGIGVMGTKLGMMSYFEPDGTVVPVTVVGFREG----NIVTQVKTEATDGYDAVQI 109
MS IG +G GM V+ + GF G N +V + +
Sbjct: 122 MSKTNKIGFVGKAAGMEI------PVMLSFIYGFEAGAKYVNPDIEVVVKYAGTFSDPAK 175
Query: 110 GY 111
G
Sbjct: 176 GK 177
>gnl|CDD|129046 smart00810, Alpha-amyl_C2, Alpha-amylase C-terminal beta-sheet
domain. This entry represents the beta-sheet domain
that is found in several alpha-amylases, usually at the
C-terminus. This domain is organised as a five-stranded
anti-parallel beta-sheet.
Length = 61
Score = 26.5 bits (59), Expect = 3.3
Identities = 16/43 (37%), Positives = 18/43 (41%), Gaps = 6/43 (13%)
Query: 233 KLKIVKIDNDLRVVMIKGAVPGKPGNLLRVAPAKIVGKNIPKN 275
LKI+ + DL V MI V K G P VG IP
Sbjct: 10 SLKILAAEADLYVAMIDEKVIMKIG------PRYDVGNLIPSG 46
>gnl|CDD|184795 PRK14698, PRK14698, V-type ATP synthase subunit A; Provisional.
Length = 1017
Score = 28.1 bits (62), Expect = 6.0
Identities = 30/121 (24%), Positives = 52/121 (42%), Gaps = 25/121 (20%)
Query: 81 PVTVVGFREGNIVTQVKTEATDGYDA--VQIGYRRVRDKKLT---KPELGHLQKSGL--- 132
P+T+ G+++G IV T G A ++I R R K+T K G + K GL
Sbjct: 285 PITLYGYKDGKIVEIKATHVYKGASAGMIEIKTRTGRKIKVTPIHKLFTGRVTKDGLEIE 344
Query: 133 -IPMRHLQE----FRLQSIDGFE-----------AGQKLAFEEIFNEGDLVDVSGTTIGK 176
+ + +++ + IDG E G+K+ ++ +E +L + G I
Sbjct: 345 EVMAKDIKKGDRIAVAKKIDGGERVKLNIRVDQKRGKKIKIPDVLDE-ELAEFLGYLIAD 403
Query: 177 G 177
G
Sbjct: 404 G 404
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.138 0.404
Gapped
Lambda K H
0.267 0.0739 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,191,703
Number of extensions: 1373455
Number of successful extensions: 1068
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1051
Number of HSP's successfully gapped: 18
Length of query: 275
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 179
Effective length of database: 6,679,618
Effective search space: 1195651622
Effective search space used: 1195651622
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.1 bits)